Lab 11: Interactive Visualization

Author

Isabella Villanueva

Learning Goals

Read in and process the COVID dataset from the New York Times GitHub repository
Create interactive graphs of different types using plot_ly() and ggplotly() functions
Customize the hoverinfo and other plot features
Create a Choropleth map using plot_geo()

Lab Description

We will work with COVID data downloaded from the New York Times. The dataset consists of COVID-19 cases and deaths in each US state during the course of the COVID epidemic.

The objective of this lab is to explore relationships between cases, deaths, and population sizes of US states, and plot data to demonstrate this

I. Reading and processing the New York Times (NYT) state-level COVID-19 data

1. Read in the data

Read in the COVID data with data.table:fread() from the NYT GitHub repository: “https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv”
Read in the state population data with data.table:fread() from the repository: “https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv”
Merge datasets

Reading the data

## data extracted from New York Times state-level data from NYT Github repository
# https://github.com/nytimes/covid-19-data

cv_states <- read_csv("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv", show_col_types = FALSE)

## state-level population information from us_census_data available on GitHub repository:
# https://github.com/COVID19Tracking/associated-data/tree/master/us_census_data

state_pops <- read_csv("https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv", show_col_types = FALSE)

Loading and Merging the data

# load COVID state-level data from NYT
cv_states <- as.data.frame(data.table::fread("https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv"))

# load state population data
state_pops <- as.data.frame(data.table::fread("https://raw.githubusercontent.com/COVID19Tracking/associated-data/master/us_census_data/us_census_2018_population_estimates_states.csv"))
state_pops$abb <- state_pops$state
state_pops$state <- state_pops$state_name
state_pops$state_name <- NULL

# merging the data
cv_states <- merge(cv_states, state_pops, by="state")

2. Look at the data

Inspect the dimensions, head, and tail of the data
Inspect the structure of each variables. Are they in the correct format?

dim(cv_states)

[1] 58094     9

head(cv_states)

    state       date fips   cases deaths geo_id population pop_density abb
1 Alabama 2023-01-04    1 1587224  21263      1    4887871    96.50939  AL
2 Alabama 2020-04-25    1    6213    213      1    4887871    96.50939  AL
3 Alabama 2023-02-26    1 1638348  21400      1    4887871    96.50939  AL
4 Alabama 2022-12-03    1 1549285  21129      1    4887871    96.50939  AL
5 Alabama 2020-05-06    1    8691    343      1    4887871    96.50939  AL
6 Alabama 2021-04-21    1  524367  10807      1    4887871    96.50939  AL

tail(cv_states)

        state       date fips  cases deaths geo_id population pop_density abb
58089 Wyoming 2022-09-11   56 175290   1884     56     577737    5.950611  WY
58090 Wyoming 2022-08-21   56 173487   1871     56     577737    5.950611  WY
58091 Wyoming 2021-01-26   56  51152    596     56     577737    5.950611  WY
58092 Wyoming 2021-02-21   56  53795    662     56     577737    5.950611  WY
58093 Wyoming 2021-08-22   56  70671    809     56     577737    5.950611  WY
58094 Wyoming 2021-03-20   56  55581    693     56     577737    5.950611  WY

str(cv_states)

'data.frame':   58094 obs. of  9 variables:
 $ state      : chr  "Alabama" "Alabama" "Alabama" "Alabama" ...
 $ date       : IDate, format: "2023-01-04" "2020-04-25" ...
 $ fips       : int  1 1 1 1 1 1 1 1 1 1 ...
 $ cases      : int  1587224 6213 1638348 1549285 8691 524367 1321892 1088370 1153149 814025 ...
 $ deaths     : int  21263 213 21400 21129 343 10807 19676 16756 16826 15179 ...
 $ geo_id     : int  1 1 1 1 1 1 1 1 1 1 ...
 $ population : int  4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 ...
 $ pop_density: num  96.5 96.5 96.5 96.5 96.5 ...
 $ abb        : chr  "AL" "AL" "AL" "AL" ...

unique(cv_states$state)

 [1] "Alabama"              "Alaska"               "Arizona"             
 [4] "Arkansas"             "California"           "Colorado"            
 [7] "Connecticut"          "Delaware"             "District of Columbia"
[10] "Florida"              "Georgia"              "Hawaii"              
[13] "Idaho"                "Illinois"             "Indiana"             
[16] "Iowa"                 "Kansas"               "Kentucky"            
[19] "Louisiana"            "Maine"                "Maryland"            
[22] "Massachusetts"        "Michigan"             "Minnesota"           
[25] "Mississippi"          "Missouri"             "Montana"             
[28] "Nebraska"             "Nevada"               "New Hampshire"       
[31] "New Jersey"           "New Mexico"           "New York"            
[34] "North Carolina"       "North Dakota"         "Ohio"                
[37] "Oklahoma"             "Oregon"               "Pennsylvania"        
[40] "Puerto Rico"          "Rhode Island"         "South Carolina"      
[43] "South Dakota"         "Tennessee"            "Texas"               
[46] "Utah"                 "Vermont"              "Virginia"            
[49] "Washington"           "West Virginia"        "Wisconsin"           
[52] "Wyoming"

After checking the dimensions, structure, head and tail of the merged dataset, all of the variables are in the correct format (integers and numbers are identified correctly, data is in the correct format, character variables like state name and abbreviations are correct and matched as well).

I also inspected the state variable because 52 counts under the variable state. After using the unique() function, this is because District of Columbia and Puerto Rico were also included in the dataset. When looking at the variable geo_id, it is not sequential in its numbering as there is a numerical gap in between California (CA) and Colorado (CO) (alphabetically adjacent), yet CA is numbered 6 and CO is numbered 8. This accounts for the geo_id counting up to 56.

3. Format the data

Make date into a date variable
Make state into a factor variable
Order the data first by state, second by date
Confirm the variables are now correctly formatted
Inspect the range values for each variable. What is the date range? The range of cases and deaths?

# format the date
cv_states$date <- as.Date(cv_states$date, format="%Y-%m-%d")

# format the state and state abbreviation (abb) variables
state_list <- unique(cv_states$state)
cv_states$state <- factor(cv_states$state, levels = state_list)
abb_list <- unique(cv_states$abb)
cv_states$abb <- factor(cv_states$abb, levels = abb_list)

# order the data first by state, second by date
cv_states = cv_states[order(cv_states$state, cv_states$date),]

# Confirm the variables are now correctly formatted
str(cv_states)

'data.frame':   58094 obs. of  9 variables:
 $ state      : Factor w/ 52 levels "Alabama","Alaska",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ date       : Date, format: "2020-03-13" "2020-03-14" ...
 $ fips       : int  1 1 1 1 1 1 1 1 1 1 ...
 $ cases      : int  6 12 23 29 39 51 78 106 131 157 ...
 $ deaths     : int  0 0 0 0 0 0 0 0 0 0 ...
 $ geo_id     : int  1 1 1 1 1 1 1 1 1 1 ...
 $ population : int  4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 4887871 ...
 $ pop_density: num  96.5 96.5 96.5 96.5 96.5 ...
 $ abb        : Factor w/ 52 levels "AL","AK","AZ",..: 1 1 1 1 1 1 1 1 1 1 ...

head(cv_states)

       state       date fips cases deaths geo_id population pop_density abb
1029 Alabama 2020-03-13    1     6      0      1    4887871    96.50939  AL
597  Alabama 2020-03-14    1    12      0      1    4887871    96.50939  AL
282  Alabama 2020-03-15    1    23      0      1    4887871    96.50939  AL
12   Alabama 2020-03-16    1    29      0      1    4887871    96.50939  AL
266  Alabama 2020-03-17    1    39      0      1    4887871    96.50939  AL
78   Alabama 2020-03-18    1    51      0      1    4887871    96.50939  AL

tail(cv_states)

        state       date fips  cases deaths geo_id population pop_density abb
57902 Wyoming 2023-03-18   56 185640   2009     56     577737    5.950611  WY
57916 Wyoming 2023-03-19   56 185640   2009     56     577737    5.950611  WY
57647 Wyoming 2023-03-20   56 185640   2009     56     577737    5.950611  WY
57867 Wyoming 2023-03-21   56 185800   2014     56     577737    5.950611  WY
58057 Wyoming 2023-03-22   56 185800   2014     56     577737    5.950611  WY
57812 Wyoming 2023-03-23   56 185800   2014     56     577737    5.950611  WY

# Inspect the range values for each variable. The range of cases and deaths?
summary(cv_states)

           state            date                 fips           cases         
 Washington   : 1158   Min.   :2020-01-21   Min.   : 1.00   Min.   :       1  
 Illinois     : 1155   1st Qu.:2020-12-06   1st Qu.:16.00   1st Qu.:  112125  
 California   : 1154   Median :2021-09-11   Median :29.00   Median :  418120  
 Arizona      : 1153   Mean   :2021-09-10   Mean   :29.78   Mean   :  947941  
 Massachusetts: 1147   3rd Qu.:2022-06-17   3rd Qu.:44.00   3rd Qu.: 1134318  
 Wisconsin    : 1143   Max.   :2023-03-23   Max.   :72.00   Max.   :12169158  
 (Other)      :51184                                                          
     deaths           geo_id        population        pop_density       
 Min.   :     0   Min.   : 1.00   Min.   :  577737   Min.   :    1.292  
 1st Qu.:  1598   1st Qu.:16.00   1st Qu.: 1805832   1st Qu.:   43.659  
 Median :  5901   Median :29.00   Median : 4468402   Median :  107.860  
 Mean   : 12553   Mean   :29.78   Mean   : 6397965   Mean   :  423.031  
 3rd Qu.: 15952   3rd Qu.:44.00   3rd Qu.: 7535591   3rd Qu.:  229.511  
 Max.   :104277   Max.   :72.00   Max.   :39557045   Max.   :11490.120  
                                                     NA's   :1106       
      abb       
 WA     : 1158  
 IL     : 1155  
 CA     : 1154  
 AZ     : 1153  
 MA     : 1147  
 WI     : 1143  
 (Other):51184

#Checking the date range
min(cv_states$date)

[1] "2020-01-21"

max(cv_states$date)

[1] "2023-03-23"

#Checking the range of cases
min(cv_states$cases)

[1] 1

max(cv_states$cases)

[1] 12169158

#Checking the range of deaths
min(cv_states$deaths)

[1] 0

max(cv_states$deaths)

[1] 104277

After checking that the variables are correctly formated (they are), the data’s dates range from 2020-01-21 (January 2020) to 2023-03-23 (March 2023).

The data’s range of cases range from 1 to 12,169,158.

The data’s range of deaths range from 0 to 104,277.

4. Add `new_cases` and `new_deaths` and correct outliers

Add variables for new cases, new_cases, and new deaths, new_deaths:
- Hint: You can set new_cases equal to the difference between cases on date i and date i-1, starting on date i=2
Use plotly for EDA: See if there are outliers or values that don’t make sense for new_cases and new_deaths. Which states and which dates have strange values?
Correct outliers: Set negative values for new_cases or new_deaths to 0
Recalculate cases and deaths as cumulative sum of updated new_cases and new_deaths
Get the rolling average of new cases

# Add variables for new_cases and new_deaths:
for (i in 1:length(state_list)) {
  cv_subset = subset(cv_states, state == state_list[i])
  cv_subset = cv_subset[order(cv_subset$date),]

  # add starting level for new cases and deaths
  cv_subset$new_cases = cv_subset$cases[1]
  cv_subset$new_deaths = cv_subset$deaths[1]

  for (j in 2:nrow(cv_subset)) {
    cv_subset$new_cases[j] = cv_subset$cases[j] - cv_subset$cases[j-1]
    cv_subset$new_deaths[j] = cv_subset$deaths[j] - cv_subset$deaths[j-1]
  }

  # include in main dataset
  cv_states$new_cases[cv_states$state==state_list[i]] = cv_subset$new_cases
  cv_states$new_deaths[cv_states$state==state_list[i]] = cv_subset$new_deaths
}

# Focus on recent dates
cv_states <- cv_states %>% dplyr::filter(date >= "2021-06-01")

# Inspect outliers using plotly
p1<-ggplot(cv_states, aes(x = date, y = new_cases, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p1)

p1<-NULL # to clear from workspace

p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)

p2<-NULL # to clear from workspace

# set negative new case or death counts to 0
cv_states$new_cases[cv_states$new_cases<0] = 0
cv_states$new_deaths[cv_states$new_deaths<0] = 0

# Recalculate `cases` and `deaths` as cumulative sum of updated `new_cases` and `new_deaths`
for (i in 1:length(state_list)) {
  cv_subset = subset(cv_states, state == state_list[i])

  # add starting level for new cases and deaths
  cv_subset$cases = cv_subset$cases[1]
  cv_subset$deaths = cv_subset$deaths[1]

  for (j in 2:nrow(cv_subset)) {
    cv_subset$cases[j] = cv_subset$new_cases[j] + cv_subset$cases[j-1]
    cv_subset$deaths[j] = cv_subset$new_deaths[j] + cv_subset$deaths[j-1]
  }
  # include in main dataset
  cv_states$cases[cv_states$state==state_list[i]] = cv_subset$cases
  cv_states$deaths[cv_states$state==state_list[i]] = cv_subset$deaths
}

# Smooth new counts
cv_states$new_cases = zoo::rollmean(cv_states$new_cases, k=7, fill=NA, align='right') %>% round(digits = 0)
cv_states$new_deaths = zoo::rollmean(cv_states$new_deaths, k=7, fill=NA, align='right') %>% round(digits = 0)

# Inspect data again
p2<-ggplot(cv_states, aes(x = date, y = new_deaths, color = state)) + geom_line() + geom_point(size = .5, alpha = 0.5)
ggplotly(p2)

#p2=NULL

Which states and which dates have strange values? (before recalculating)

New cases

Florida, 2021-06-04 with -40527 new cases
Colorado, 2022-01-29 with -4678 new cases
Pennsylvania, 2022-02-08 with -4397 new cases
Texas, 2022-10-08 with -11187 new cases
Kentucky, 2022-10-11 with -8829 new cases
Tennessee, 2023-01-01 with -18255 new cases

New deaths

California, 2021-06-04 with -375 cases
California, 2021-08-11 with -357 cases
Massachusetts, 2022-03-14 with -3370 new deaths

After recalculating cases and deaths as cumulative sum of updated new_cases and new_deaths, the strange values that were negative are no longer apparent on the new graph plots, making the peaks of new cases and new deaths more visible and helping those analyzing the data to focus on the intended data.

5. Add additional variables

Add population-normalized (by 100,000) variables for each variable type (rounded to 1 decimal place). Make sure the variables you calculate are in the correct format (numeric). You can use the following variable names:
- per100k = cases per 100,000 population
- newper100k= new cases per 100,000
- deathsper100k = deaths per 100,000
- newdeathsper100k = new deaths per 100,000
Add a “naive CFR” variable representing deaths / cases on each date for each state
Create a dataframe representing values on the most recent date, cv_states_today, as done in lecture

# add population normalized (by 100,000) counts for each variable
cv_states$per100k =  as.numeric(format(round(cv_states$cases/(cv_states$population/100000),1),nsmall=1))
cv_states$newper100k =  as.numeric(format(round(cv_states$new_cases/(cv_states$population/100000),1),nsmall=1))
cv_states$deathsper100k =  as.numeric(format(round(cv_states$deaths/(cv_states$population/100000),1),nsmall=1))
cv_states$newdeathsper100k =  as.numeric(format(round(cv_states$new_deaths/(cv_states$population/100000),1),nsmall=1))

# add a naive_CFR variable = deaths / cases
cv_states = cv_states %>% mutate(naive_CFR = round((deaths*100/cases),2))

# create a `cv_states_today` variable
cv_states_today = subset(cv_states, date==max(cv_states$date))

II. Scatterplots

6. Explore scatterplots using `plot_ly()`

Create a scatterplot using plot_ly() representing pop_density vs. various variables (e.g. cases, per100k, deaths, deathsper100k) for each state on most recent date (cv_states_today)
- Size the points by state population
- Use hover to identify any outliers.
- Remove those outliers and replot.
Choose one plot. For this plot:
- Add hoverinfo specifying the state name, cases per 100k, and deaths per 100k, similarly to how we did this in the lecture notes
- Add layout information to title the chart and the axes
- Enable hovermode = "compare"

# pop_density vs. cases
cv_states_today %>% 
  plot_ly(x = ~pop_density, y = ~cases, 
          type = 'scatter', mode = 'markers', color = ~state,
          size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))

# filter out "District of Columbia"
cv_states_today_scatter <- cv_states_today %>% filter(state!="District of Columbia")

# pop_density vs. cases after filtering
cv_states_today_scatter %>% 
  plot_ly(x = ~pop_density, y = ~cases, 
          type = 'scatter', mode = 'markers', color = ~state,
          size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))

# pop_density vs. deathsper100k
cv_states_today_scatter %>% 
  plot_ly(x = ~pop_density, y = ~deathsper100k, 
          type = 'scatter', mode = 'markers', color = ~state,
          size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5))

# Adding hoverinfo
cv_states_today_scatter %>% 
  plot_ly(x = ~pop_density, y = ~deathsper100k,
          type = 'scatter', mode = 'markers', color = ~state,
          size = ~population, sizes = c(5, 70), marker = list(sizemode='diameter', opacity=0.5),
          hoverinfo = 'text',
          text = ~paste( paste(state, ":", sep=""), paste(" Cases per 100k: ", per100k, sep="") , 
                         paste(" Deaths per 100k: ",
                        deathsper100k, sep=""), sep = "<br>")) %>%
  layout(title = "Population-normalized COVID-19 deaths (per 100k) vs. population density for US states",
                  yaxis = list(title = "Deaths per 100k"), xaxis = list(title = "Population Density"),
         hovermode = "compare")

7. Explore scatterplot trend interactively using `ggplotly()` and `geom_smooth()`

For pop_density vs. newdeathsper100k create a chart with the same variables using gglot_ly()
Explore the pattern between \(x\) and \(y\) using geom_smooth()
- Explain what you see. Do you think pop_density is a correlate of newdeathsper100k?

It’s possible that population density could correlate with newdeathsper100k, but the non-linear pattern implies other factors may be at play. In this scatter plot, we see the relationship between population density (pop_density on the x-axis) and new deaths per 100,000 people (newdeathsper100k on the y-axis). The data points are represented by black circles, with larger circles potentially indicating higher frequencies or weights of observations. A blue line represents a smoothed trend, with a shaded area indicating confidence intervals around this trend.

Observations

Initial Decrease: Atlow population densities, there appears to be a slight decrease in newdeathsper100k, showing a downward trend until around a pop_density just before 250.
Increase and Plateau: Around a pop_density of 250-500, there is an increase in newdeathsper100k, followed by a somewhat stable region where the death rate doesn’t change drastically with increasing density.
Decreasing Arch: Beyond a pop_density of around 750, there is a noticeable downward trend in newdeathsper100k, with both the blue trend line and individual points indicating fewer deaths per 100,000 people as density increases.

Interpretation

This pattern suggests that population density has a non-linear association with newdeathsper100k. While there may be some correlation, it is complex and may be influenced by other variables.

p <- ggplot(cv_states_today_scatter, aes(x=pop_density, y=newdeathsper100k, size=population)) + geom_point() + geom_smooth()
ggplotly(p)

8. Multiple line chart

Create a line chart of the naive_CFR for all states over time using plot_ly()
- Use the zoom and pan tools to inspect the naive_CFR for the states that had an increase in September. How have they changed over time? Over time, the general trend of this line chart shows a general decrease over the span of about 2 years, with a drastic drop around January 2022. Then a plateau can be seen afterward.
Create one more line chart, for Florida only, which shows new_cases and new_deaths together in one plot. Hint: use add_layer() (this function did not work, add_trace did)
- Use hoverinfo to “eyeball” the approximate peak of deaths and peak of cases. What is the time delay between the peak of cases and the peak of deaths?

The peak date of deaths was September 20, 2021 with 445 deaths where as the peak date of cases was January 10, 2022 with 84.669K cases. The time delay is about 112 days between these two peaks.

# Line chart for naive_CFR for all states over time using `plot_ly()`
plot_ly(cv_states, x = ~date, y = ~naive_CFR, color = ~state, type = "scatter", mode = "lines")

Warning in RColorBrewer::brewer.pal(N, "Set2"): n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors
Warning in RColorBrewer::brewer.pal(N, "Set2"): n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

# Line chart for Florida showing new_cases and new_deaths together
cv_states %>% 
  filter(state == "Florida") %>% 
  plot_ly(x = ~date, y = ~new_cases, type = "scatter", mode = "lines", name = "New Cases") %>%
  add_trace(y = ~new_deaths, type = "scatter", mode = "lines", name = "New Deaths")

9. Heatmaps

Create a heatmap to visualize new_cases for each state on each date greater than June 1st, 2021 - Start by mapping selected features in the dataframe into a matrix using the tidyr package function pivot_wider(), naming the rows and columns, as done in the lecture notes

Use plot_ly() to create a heatmap out of this matrix. Which states stand out?

In this initial heatmap, California, Florida, New York, and Texas are the only states that stand out.

Repeat with newper100k variable. Now which states stand out?

With the newper100k variable, there is a general standard hue amongst all states except Rhode Island, which stands out with its vivid color.

Create a second heatmap in which the pattern of new_cases for each state over time becomes more clear by filtering to only look at dates every two weeks

With this step, it is apparent which states and which time frames are peaks of new cases with the bright yellow color highlighting these time periods and locations. For example, Aug 2021 in Louisiana and Mississippi, Sept 2021 in South Carolina and Tennessee, and Oct 2021 in Alaska are states with prominent values.

# Map state, date, and new_cases to a matrix
library(tidyr)
cv_states_mat <- cv_states %>% select(state, date, new_cases) %>% dplyr::filter(date>as.Date("2021-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = new_cases))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)

# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
             z=~cv_states_mat2,
             type="heatmap",
             showscale=T)

# Repeat with newper100k
cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% dplyr::filter(date>as.Date("2021-06-15"))
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = newper100k))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)

plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
             z=~cv_states_mat2,
             type="heatmap",
             showscale=T)

# Create a second heatmap after filtering to only include dates every other week
filter_dates <- seq(as.Date("2021-06-15"), as.Date("2021-11-01"), by="2 weeks")

cv_states_mat <- cv_states %>% select(state, date, newper100k) %>% filter(date %in% filter_dates)
cv_states_mat2 <- as.data.frame(pivot_wider(cv_states_mat, names_from = state, values_from = newper100k))
rownames(cv_states_mat2) <- cv_states_mat2$date
cv_states_mat2$date <- NULL
cv_states_mat2 <- as.matrix(cv_states_mat2)

# Create a heatmap using plot_ly()
plot_ly(x=colnames(cv_states_mat2), y=rownames(cv_states_mat2),
             z=~cv_states_mat2,
             type="heatmap",
             showscale=T)

10. Map

Create a map to visualize the naive_CFR by state on October 15, 2021
Compare with a map visualizing the naive_CFR by state on most recent date
Plot the two maps together using subplot(). Make sure the shading is for the same range of values (google is your friend for this)
Describe the difference in the pattern of the CFR.

In the plotting of the two maps, one by state on October 15, 2021 and the other by state on November 12, 2024, there is a drastic difference between these two maps. We can notice that the recent map has little to no hue, indicated a lack in new cases in comparison to the 2021 map. We can also notice that the northern states of Alaska, Montana, Idaho, and Wyoming have the darkest hues in their map. In comparing the two maps for their pattern of CFR, the most recent map has no pattern while there is a noticeable pattern in the 2021 map.

### For specified date
pick.date = "2021-10-15"

# Extract the data for each state by its abbreviation
cv_per100 <- cv_states %>% filter(date==pick.date) %>% select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL

# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))

# Set up mapping details
set_map_details <- list(
  scope = 'usa',
  projection = list(type = 'albers usa'),
  showlakes = TRUE,
  lakecolor = toRGB('white')
)

# Make sure both maps are on the same color scale
shadeLimit <- 125

# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>% 
  add_trace(
    z = ~newper100k, text = ~hover, locations = ~state,
    color = ~newper100k, colors = 'Purples'
  )
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", pick.date), limits = c(0,shadeLimit))
fig <- fig %>% layout(
    title = paste('Cases per 100k by State as of ', pick.date, '<br>(Hover for value)'),
    geo = set_map_details
  )
fig_pick.date <- fig

#############
### Map for today's date

# Extract the data for each state by its abbreviation
cv_per100 <- cv_states_today %>%  select(state, abb, newper100k, cases, deaths) # select data
cv_per100$state_name <- cv_per100$state
cv_per100$state <- cv_per100$abb
cv_per100$abb <- NULL

# Create hover text
cv_per100$hover <- with(cv_per100, paste(state_name, '<br>', "Cases per 100k: ", newper100k, '<br>', "Cases: ", cases, '<br>', "Deaths: ", deaths))

# Set up mapping details
set_map_details <- list(
  scope = 'usa',
  projection = list(type = 'albers usa'),
  showlakes = TRUE,
  lakecolor = toRGB('white')
)

# Create the map
fig <- plot_geo(cv_per100, locationmode = 'USA-states') %>% 
  add_trace(
    z = ~newper100k, text = ~hover, locations = ~state,
    color = ~newper100k, colors = 'Purples'
  )
fig <- fig %>% colorbar(title = paste0("Cases per 100k: ", Sys.Date()), limits = c(0,shadeLimit))
fig <- fig %>% layout(
    title = paste('Cases per 100k by State as of', Sys.Date(), '<br>(Hover for value)'),
    geo = set_map_details
  )
fig_Today <- fig


### Plot together 
subplot(fig_pick.date, fig_Today, nrows = 2, margin = .05)